it's called mris_ca_label, and yes, that is what I mean. If you tell us
your hardware/software environment Zeke can get you a binary
On Thu, 28 Jan 2016,
Fengji Geng wrote:
Hi Bruce,
Did you mean an updated version of mri_parcellate? If so, it would be great.
Thanks!
--------------------------------------------
Hi Fengji
this is a known bug in mris_parcellate. We can give you an updated version
if you want, but you should probably rerun all your subjects using it. The
good news is that it's fast - just a couple of min/hemi
cheers
Bruce
On Tue, 26 Jan
2016, Fengji Geng wrote:
> Hello fs experts,
>
> We ran a command like ?recon-all -all -s HMN002
-hippocampal-subfields-T1T2
> HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)?
> (which is also attached below). The error log file is also attached here.?
>
> Error msg:
>---------------------------------------------------------------------------
> --------------------------
> setting seed for random number generator to 1234
> using ../mri/aseg.presurf.mgz aseg volume to correct midline
> $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
> ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $
> reading
atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.f
ille
> d.desikan_killiany.2010-03-25.gcs...
> reading color table from GCSA file....
> average std = 1.0?? using min determinant for regularization = 0.011
> 0 singular and 384 ill-conditioned covariance matrices regularized
> input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
> labeling surface...
> 1592 labels changed using aseg
> relabeling using gibbs priors...
> 000:?? 2975 changed, 134786 examined...
> 001:??? 698 changed, 12707 examined...
> 002:??? 152 changed, 3873 examined...
> 003:???? 50 changed, 880 examined...
> 004:???? 29 changed, 284 examined...
> 005:???? 16 changed, 164 examined...
> 006:????? 7 changed, 87 examined...
> 007:????? 1 changed, 42 examined...
> 008:????? 0 changed, 4 examined...
> 206 labels changed using aseg
> 000: 105 total segments, 64 labels (264 vertices) changed
> 001: 43 total segments, 4 labels (14 vertices) changed
> 002: 39 total segments, 0 labels (0 vertices) changed
> 1 filter iterations complete (10 requested, 0 changed)
> Abort (core dumped)
> Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23
> 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016
>
> Our freesurfer information:
> -------- freesurfer-Linux-centos6_x86_64-dev-20151215 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys
> FSFAST_HOME?????? /cell_root/software/freesurfer/dev/sys/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR????? /export/data/hippocampus/HMN/data
> MNI_DIR?????????? /cell_root/software/freesurfer/dev/sys/mni
> FSL_DIR?????????? /cell_root/software/fsl/new/sys
>
> Looking forward to hearing how we can resolve this error. Also, thanks in
> advance.
>
> Best,
>
> ----- Fengji
>
>
>
---
Fengji
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